The ISME Journal (2015) 9, 2671–2681 © 2015 International Society for Microbial Ecology All rights reserved 1751-7362/15 www.nature.com/ismej ORIGINAL ARTICLE Soil-foraging animals alter the composition and co-occurrence of microbial communities in a desert shrubland David J Eldridge1, Jason N Woodhouse2, Nathalie JA Curlevski2,3, Matthew Hayward4,5, Mark V Brown2 and Brett A Neilan2 1Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of NSW, Sydney, NSW, Australia; 2School of Biotechnology and Biomolecular Sciences, University of NSW, Sydney, NSW, Australia; 3Faculty of Science, Aquatic Processes Group, University of Technology, Ultimo, NSW, Australia; 4Australian Wildlife Conservancy, Nichols Point, VIC, Australia and 5School of Environment, Natural Resources and Geography; and School of Biological Science, Bangor University, Bangor, UK Animals that modify their physical environment by foraging in the soil can have dramatic effects on ecosystem functions and processes. We compared bacterial and fungal communities in the foraging pits created by bilbies and burrowing bettongs with undisturbed surface soils dominated by biocrusts. Bacterial communities were characterized by Actinobacteria and Alphaproteobacteria, and fungal communities by Lecanoromycetes and Archaeosporomycetes. The composition of bacterial or fungal communities was not observed to vary between loamy or sandy soils. There were no differences in richness of either bacterial or fungal operational taxonomic units (OTUs) in the soil of young or old foraging pits, or undisturbed soils. Although the bacterial assemblage did not vary among the three microsites, the composition of fungi in undisturbed soils was significantly different from that in old or young foraging pits. Network analysis indicated that a greater number of correlations between bacterial OTUs occurred in undisturbed soils and old pits, whereas a greater number of correlations between fungal OTUs occurred in undisturbed soils. Our study suggests that digging by soil-disturbing animals is likely to create successional shifts in soil microbial and fungal communities, leading to functional shifts associated with the decomposition of organic matter and the fixation of nitrogen. Given the primacy of organic matter decomposition in arid and semi-arid environments, the loss of native soil-foraging animals is likely to impair the ability of these systems to maintain key ecosystem processes such as the mineralization of nitrogen and the breakdown of organic matter, and to recover from disturbance. The ISME Journal (2015) 9, 2671–2681; doi:10.1038/ismej.2015.70; published online 1 May 2015 Introduction with exotic pests including the European rabbit (Oryctolagus cuniculus) and predation by introduced Australia has suffered one of the highest rates of species such as the domestic cat (Felis catus) and the global mammal extinctions over the past 200 years red fox (Vulpes vulpes) (Johnson, 2006). Two species since European settlement (Woinarski et al., 2012). that have suffered substantial range restrictions are Losses have been most pronounced in the critical – the greater bilby (Macrotis lagotis) and the burrowing weight range (35 5500 g) mammals, which were bettong (Bettongia lesueur). Recent attempts have once common over large areas of continental been made to reintroduce these animals into Australia (Johnson, 2006). The loss of these animals, predator-proof exclosures within their former range or the contraction of their ranges, has been attributed in an effort to re-establish viable populations (James to multiple causes associated with European and Eldridge, 2007). settlement and pastoral practices such as altered Many of Australia’s locally extinct animals forage fire regimes, overgrazing by livestock, competition extensively in the soil for seeds, bulbs, invertebrates and fungi (Robley et al., 2001; James et al., 2011; Eldridge et al., 2012). Foraging disturbs the soil Correspondence: DJ Eldridge, Centre for Ecosystem Science, School surface and breaks up the surface crust (biocrust), of Biological, Earth and Environmental Sciences, University of altering rates of water infiltration, and creating small NSW, Sydney, NSW 2052, Australia. E-mail: [email protected] pits and depressions that trap water, soil, organic Received 5 October 2014; revised 5 February 2015; accepted matter and seed (James et al., 2009). These pits 25 March 2015; published online 1 May 2015 develop into patches of higher nutrients, with greater Animal foraging alters microbial community DJ Eldridge et al 2672 concentrations of plant-available nitrogen and This compares with young pits (o3 months old), carbon than the surrounding soil matrix (James which have relatively low levels of litter and organic et al., 2010) and often a different vegetation commu- matter (D J Eldridge, unpublished data). We would nity (Lavelle et al., 2006). Studies worldwide have expect pit age to influence microbial community shown that modification of the abiotic environment structure, as these old pits (~12 months) would have by these animals, a process referred to as ecosystem more time to establish seedlings and accumulate engineering (sensu Jones et al., 1994), alters litter and microorganisms that are present on energy flows and resource availability, increases adjacent, undisturbed surfaces. Furthermore, older species richness, diversity and productivity, through pits could provide a greater range of different niche construction, ultimately controlling the environments, with differences in depth, shape availability and distribution of resources to other and orientation, and therefore different soil chem- organisms (for example, Whitford and Kay, 1999; istry and organic matter at varying stages of Jones et al., 2010). decomposition. An important process moderated by soil- We compared the community structure of soil disturbing animals in arid environments is the microbial communities in old and young pits with decomposition of organic matter. Litter and organic the undisturbed surface soil on two soil types in an matter in these systems are spatially and temporally area where bilbies and bettongs have been reintro- variable, and is often concentrated within the duced into their former range. Both bilbies and foraging pits of animals (James and Eldridge, 2007). bettongs construct pits while foraging for buried Litter is a source of carbon, nitrogen and other trace seed, invertebrates and plant roots. The pits of these elements, and provides habitat for a range of micro- two species are indistinguishable, and range from and macro-invertebrates involved in the decomposi- cylindrical-shaped excavations about 15-cm wide tion of organic matter (Haslem et al., 2011). Litter and up to 20-cm deep to shallow basin-like struc- falling into pits comes into close contact with soil, tures (Eldridge et al., 2012). Pits are constructed only where it is held in situ more effectively than if it once, and unlike cache pits of heteromyid rodents remained on the soil surface where it is subject to (Geluso, 2005), are rarely reworked. Because pits removal by wind and water (Whitford, 2002). vary in depth and shape, and are constructed in soils Together with reduced evaporation resulting from of different texture, they provide a range of different lower temperatures in the pits than the undisturbed physical environments that influences the trapping surface (Eldridge and Mensinga, 2007), this increases and retention of litter and the breakdown of organic the time period over which soil moisture is optimum matter. for microbial decomposition and nutrient minerali- We hypothesized that the microbial community in zation (Steinberger and Whitford, 1983; Jacobsen and pit soils would support more microorganisms com- Jacobsen, 1998; Whitford, 2002). Litter remaining on monly associated with decomposing litter. Conver- the surface, however, is subject to photodegradation sely, we expected that the microbial community (Austin and Vivanco, 2006), potentially reducing the composition in undisturbed soils would support a return of carbon to the soil organic pool. community dominated by cyanobacteria, given the Soil-disturbing animals therefore play an impor- extensive cover of biocrusts on the soil surface. We tant role in bringing surface-resident organic matter used microbial network analysis to examine the into contact with soil microorganisms. The accumu- structure of microbial communities, particularly in lation of litter in the pits is also likely to exert a relation to resilience and reactivity (Ruiz-Moreno strong selective pressure on microorganisms essen- et al., 2006; Bissett et al., 2013). Examination of tial for the decomposition process. Given the marked microbial networks improves our understanding of differences in the biotic (litter cover and composi- why undisturbed soils might be resistant to nutrient tion) and abiotic (for example, surface temperature, amendment, how microbial community structure is soil moisture) environments between pits and altered following pit construction, and how digging undisturbed soils, that is, those soils undisturbed promotes nutrient enrichment within these micro- by animal activity (for example, Vossbrinck et al., sites (James et al., 2009). 1979; Wallwork et al., 1985; Eldridge and Mensinga, 2007), we expected that the pits would differ in the composition of soil microorganisms. For example, Materials and methods studies of foraging disturbances constructed by the short-beaked echidna